|
| Status |
Public on Apr 07, 2021 |
| Title |
Scramble M1 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: M1 macrophages
genotype: scramble shRNA
|
| Treatment protocol |
Lentiviral transduction was conducted in serum free medium containing 20% L929 supernatant with 8 μg/ml polybrene at day 3 (MOI = 30). For BMDMs were stimulated with 1000 ng/ml LPS and 20 ng/ml IFNγfor 6 hours.
|
| Growth protocol |
BMDMs were cultured in complete DMEM containing 20%L929 supernatant for 7 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cell lyses RNA was harvested using Trizol reagent. Direct-zol RNA miniPrep (Zymo Research) was used for total RNA isolation for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Total RNA extracted from M1 cells was digested to 180 bp fragments after removing rRNAs with a Ribo-Zero Gold kit (Illumina, San Diego, USA). A sequencing library was created by reverse-transcribing RNA fragments to cDNA, and ligating specific adapters at both ends of these cDNA fragments.
The sequencing libraries were loaded to the surface of flow cells, and amplified into clonal clusters through bridge amplification. All of the clusters on the flow cell were sequenced by NextSeq 500 (Illumina).
The FastQC (v0.11.8) program (http://www.bioinformatics. babraham.ac.uk/projects/fastqc/) was used to examine the quality of sequencing reads, and HISAT2 (v2.1.0) was used to align sequencing reads to mouse genome references (GRCm38).
The output SAM files were normalized and quantified with R packages Rsubread (v 2.0.0)and edgeR (v 3.28.0) from Bioconductor. A robust normalization approach, the trimmed mean of M value, was applied and log2-transformation was used to obtain the final expression values.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Apr 07, 2021 |
| Contact name |
Shi-Chuen Miaw |
| E-mail(s) |
smiaw@ntu.edu.tw
|
| Phone |
0939676785
|
| Organization name |
National Taiwan University, College of Medicine
|
| Department |
Immunology
|
| Street address |
No.1 Jen Ai road section 1
|
| City |
Taipei |
| ZIP/Postal code |
100 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE143302 |
Adenylate kinase 4 Promotes the expression of Inflammatory Genes in Macrophages via Hif-1a |
|
| Relations |
| BioSample |
SAMN13762631 |
| SRA |
SRX7521427 |
